This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 78 arm-level events and 12 clinical features across 165 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
RACE | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | |
1p gain | 12 (7%) | 153 |
0.0892 (1.00) |
0.564 (1.00) |
0.171 (1.00) |
0.0268 (1.00) |
0.444 (1.00) |
0.113 (1.00) |
0.774 (1.00) |
0.0483 (1.00) |
1 (1.00) |
0.219 (1.00) |
0.601 (1.00) |
1 (1.00) |
1q gain | 34 (21%) | 131 |
0.728 (1.00) |
0.501 (1.00) |
0.619 (1.00) |
0.0049 (1.00) |
0.282 (1.00) |
0.443 (1.00) |
0.441 (1.00) |
0.298 (1.00) |
0.604 (1.00) |
0.575 (1.00) |
0.096 (1.00) |
0.485 (1.00) |
2p gain | 41 (25%) | 124 |
0.905 (1.00) |
0.78 (1.00) |
0.411 (1.00) |
0.375 (1.00) |
0.216 (1.00) |
0.532 (1.00) |
0.0311 (1.00) |
0.0222 (1.00) |
0.639 (1.00) |
0.103 (1.00) |
0.869 (1.00) |
0.11 (1.00) |
2q gain | 43 (26%) | 122 |
0.915 (1.00) |
0.964 (1.00) |
0.299 (1.00) |
0.259 (1.00) |
0.14 (1.00) |
0.623 (1.00) |
0.0332 (1.00) |
0.0206 (1.00) |
0.183 (1.00) |
0.146 (1.00) |
0.546 (1.00) |
0.0118 (1.00) |
3p gain | 27 (16%) | 138 |
0.55 (1.00) |
0.819 (1.00) |
0.183 (1.00) |
0.836 (1.00) |
0.395 (1.00) |
0.0364 (1.00) |
0.533 (1.00) |
0.698 (1.00) |
0.255 (1.00) |
0.886 (1.00) |
0.209 (1.00) |
1 (1.00) |
3q gain | 34 (21%) | 131 |
0.899 (1.00) |
0.992 (1.00) |
0.271 (1.00) |
0.687 (1.00) |
0.489 (1.00) |
0.0489 (1.00) |
0.441 (1.00) |
0.302 (1.00) |
0.604 (1.00) |
0.725 (1.00) |
0.29 (1.00) |
0.703 (1.00) |
4p gain | 9 (5%) | 156 |
0.819 (1.00) |
0.914 (1.00) |
0.22 (1.00) |
0.65 (1.00) |
0.245 (1.00) |
0.338 (1.00) |
0.18 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0445 (1.00) |
1 (1.00) |
4q gain | 5 (3%) | 160 |
0.989 (1.00) |
0.857 (1.00) |
0.898 (1.00) |
1 (1.00) |
0.708 (1.00) |
0.729 (1.00) |
0.0626 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.439 (1.00) |
|
5p gain | 36 (22%) | 129 |
0.509 (1.00) |
0.699 (1.00) |
0.774 (1.00) |
0.157 (1.00) |
0.715 (1.00) |
0.662 (1.00) |
0.092 (1.00) |
0.0412 (1.00) |
0.119 (1.00) |
0.401 (1.00) |
0.532 (1.00) |
0.242 (1.00) |
5q gain | 24 (15%) | 141 |
0.752 (1.00) |
0.936 (1.00) |
0.231 (1.00) |
0.58 (1.00) |
0.283 (1.00) |
0.892 (1.00) |
0.386 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.536 (1.00) |
0.211 (1.00) |
0.334 (1.00) |
6p gain | 41 (25%) | 124 |
0.286 (1.00) |
0.774 (1.00) |
0.209 (1.00) |
0.279 (1.00) |
0.0233 (1.00) |
0.0464 (1.00) |
0.588 (1.00) |
0.187 (1.00) |
0.034 (1.00) |
0.441 (1.00) |
0.0285 (1.00) |
0.0447 (1.00) |
6q gain | 36 (22%) | 129 |
0.516 (1.00) |
0.917 (1.00) |
0.0419 (1.00) |
0.297 (1.00) |
0.052 (1.00) |
0.0234 (1.00) |
0.576 (1.00) |
0.0734 (1.00) |
0.021 (1.00) |
0.256 (1.00) |
0.0709 (1.00) |
0.0329 (1.00) |
7p gain | 102 (62%) | 63 |
0.289 (1.00) |
0.628 (1.00) |
0.0268 (1.00) |
0.436 (1.00) |
0.15 (1.00) |
0.797 (1.00) |
0.63 (1.00) |
0.00466 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.0454 (1.00) |
0.766 (1.00) |
7q gain | 85 (52%) | 80 |
0.451 (1.00) |
0.504 (1.00) |
0.00502 (1.00) |
0.547 (1.00) |
0.0658 (1.00) |
0.419 (1.00) |
0.534 (1.00) |
0.00748 (1.00) |
1 (1.00) |
0.171 (1.00) |
0.085 (1.00) |
0.224 (1.00) |
8p gain | 42 (25%) | 123 |
0.326 (1.00) |
0.786 (1.00) |
0.182 (1.00) |
0.206 (1.00) |
0.697 (1.00) |
0.593 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.521 (1.00) |
1 (1.00) |
8q gain | 89 (54%) | 76 |
0.108 (1.00) |
0.702 (1.00) |
0.00827 (1.00) |
0.114 (1.00) |
0.11 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.0896 (1.00) |
0.219 (1.00) |
0.0813 (1.00) |
0.189 (1.00) |
0.517 (1.00) |
9p gain | 42 (25%) | 123 |
0.146 (1.00) |
0.338 (1.00) |
0.282 (1.00) |
0.842 (1.00) |
0.717 (1.00) |
0.79 (1.00) |
1 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.898 (1.00) |
0.731 (1.00) |
9q gain | 33 (20%) | 132 |
0.136 (1.00) |
0.199 (1.00) |
0.026 (1.00) |
0.936 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.439 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.86 (1.00) |
0.889 (1.00) |
0.681 (1.00) |
10p gain | 13 (8%) | 152 |
0.762 (1.00) |
0.88 (1.00) |
0.875 (1.00) |
0.42 (1.00) |
0.932 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.603 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.575 (1.00) |
0.453 (1.00) |
10q gain | 7 (4%) | 158 |
0.532 (1.00) |
0.51 (1.00) |
0.698 (1.00) |
0.679 (1.00) |
0.876 (1.00) |
1 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.232 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.284 (1.00) |
11p gain | 32 (19%) | 133 |
0.555 (1.00) |
0.326 (1.00) |
0.868 (1.00) |
0.631 (1.00) |
0.458 (1.00) |
0.755 (1.00) |
0.845 (1.00) |
0.0724 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.587 (1.00) |
0.0267 (1.00) |
11q gain | 26 (16%) | 139 |
0.398 (1.00) |
0.13 (1.00) |
0.838 (1.00) |
0.439 (1.00) |
0.258 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.129 (1.00) |
0.591 (1.00) |
0.792 (1.00) |
0.297 (1.00) |
0.0104 (1.00) |
12p gain | 33 (20%) | 132 |
0.758 (1.00) |
0.421 (1.00) |
0.801 (1.00) |
0.438 (1.00) |
0.39 (1.00) |
0.639 (1.00) |
0.699 (1.00) |
0.298 (1.00) |
0.0951 (1.00) |
0.392 (1.00) |
0.503 (1.00) |
0.166 (1.00) |
12q gain | 24 (15%) | 141 |
0.171 (1.00) |
0.21 (1.00) |
0.863 (1.00) |
0.708 (1.00) |
0.558 (1.00) |
0.943 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.265 (1.00) |
0.648 (1.00) |
13q gain | 113 (68%) | 52 |
0.451 (1.00) |
0.67 (1.00) |
0.37 (1.00) |
0.325 (1.00) |
0.0328 (1.00) |
0.0403 (1.00) |
0.506 (1.00) |
0.000593 (0.552) |
1 (1.00) |
0.955 (1.00) |
0.0199 (1.00) |
0.102 (1.00) |
14q gain | 8 (5%) | 157 |
0.246 (1.00) |
0.894 (1.00) |
0.683 (1.00) |
1 (1.00) |
0.394 (1.00) |
0.821 (1.00) |
0.472 (1.00) |
1 (1.00) |
0.261 (1.00) |
1 (1.00) |
0.642 (1.00) |
1 (1.00) |
15q gain | 3 (2%) | 162 |
0.812 (1.00) |
0.922 (1.00) |
0.0863 (1.00) |
0.0489 (1.00) |
0.172 (1.00) |
1 (1.00) |
0.0956 (1.00) |
0.227 (1.00) |
1 (1.00) |
1 (1.00) |
0.218 (1.00) |
|
16p gain | 41 (25%) | 124 |
0.498 (1.00) |
0.777 (1.00) |
0.122 (1.00) |
0.78 (1.00) |
0.323 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.0222 (1.00) |
0.163 (1.00) |
0.393 (1.00) |
0.294 (1.00) |
0.401 (1.00) |
16q gain | 41 (25%) | 124 |
0.926 (1.00) |
0.853 (1.00) |
0.463 (1.00) |
0.933 (1.00) |
0.161 (1.00) |
0.392 (1.00) |
0.857 (1.00) |
0.0222 (1.00) |
0.163 (1.00) |
0.626 (1.00) |
0.215 (1.00) |
0.0954 (1.00) |
17p gain | 8 (5%) | 157 |
0.292 (1.00) |
0.544 (1.00) |
0.638 (1.00) |
0.0398 (1.00) |
0.704 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.503 (1.00) |
1 (1.00) |
1 (1.00) |
0.859 (1.00) |
1 (1.00) |
17q gain | 32 (19%) | 133 |
0.216 (1.00) |
0.581 (1.00) |
0.81 (1.00) |
0.949 (1.00) |
0.604 (1.00) |
0.417 (1.00) |
0.556 (1.00) |
0.469 (1.00) |
0.598 (1.00) |
0.463 (1.00) |
0.748 (1.00) |
0.692 (1.00) |
18p gain | 8 (5%) | 157 |
0.552 (1.00) |
0.425 (1.00) |
0.0398 (1.00) |
0.372 (1.00) |
0.496 (1.00) |
0.278 (1.00) |
0.727 (1.00) |
0.131 (1.00) |
0.261 (1.00) |
0.152 (1.00) |
0.104 (1.00) |
0.0686 (1.00) |
18q gain | 6 (4%) | 159 |
0.0244 (1.00) |
0.391 (1.00) |
0.0278 (1.00) |
0.165 (1.00) |
0.083 (1.00) |
0.141 (1.00) |
0.219 (1.00) |
0.406 (1.00) |
0.202 (1.00) |
0.047 (1.00) |
0.00409 (1.00) |
0.0674 (1.00) |
19p gain | 33 (20%) | 132 |
0.742 (1.00) |
0.441 (1.00) |
0.847 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.559 (1.00) |
0.0718 (1.00) |
0.601 (1.00) |
0.498 (1.00) |
0.788 (1.00) |
0.183 (1.00) |
19q gain | 32 (19%) | 133 |
0.179 (1.00) |
0.491 (1.00) |
0.931 (1.00) |
0.182 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.694 (1.00) |
0.0724 (1.00) |
0.598 (1.00) |
0.249 (1.00) |
0.639 (1.00) |
0.0922 (1.00) |
20p gain | 109 (66%) | 56 |
0.423 (1.00) |
0.183 (1.00) |
0.0103 (1.00) |
0.776 (1.00) |
0.332 (1.00) |
0.904 (1.00) |
0.1 (1.00) |
0.0328 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.335 (1.00) |
0.415 (1.00) |
20q gain | 145 (88%) | 20 |
0.123 (1.00) |
0.14 (1.00) |
0.117 (1.00) |
0.566 (1.00) |
0.0304 (1.00) |
0.705 (1.00) |
0.812 (1.00) |
0.000953 (0.886) |
0.545 (1.00) |
0.181 (1.00) |
0.108 (1.00) |
0.0991 (1.00) |
21q gain | 10 (6%) | 155 |
0.395 (1.00) |
0.482 (1.00) |
0.528 (1.00) |
0.742 (1.00) |
0.905 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.899 (1.00) |
1 (1.00) |
22q gain | 9 (5%) | 156 |
0.0302 (1.00) |
0.858 (1.00) |
0.615 (1.00) |
0.698 (1.00) |
0.389 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.357 (1.00) |
1 (1.00) |
xq gain | 34 (21%) | 131 |
0.921 (1.00) |
0.284 (1.00) |
0.773 (1.00) |
0.207 (1.00) |
0.434 (1.00) |
0.595 (1.00) |
0.441 (1.00) |
0.469 (1.00) |
0.347 (1.00) |
0.927 (1.00) |
0.613 (1.00) |
0.689 (1.00) |
1p loss | 46 (28%) | 119 |
0.565 (1.00) |
0.549 (1.00) |
0.9 (1.00) |
0.722 (1.00) |
0.552 (1.00) |
0.901 (1.00) |
0.489 (1.00) |
0.0203 (1.00) |
0.35 (1.00) |
0.885 (1.00) |
0.282 (1.00) |
0.101 (1.00) |
1q loss | 26 (16%) | 139 |
0.617 (1.00) |
0.658 (1.00) |
0.651 (1.00) |
0.731 (1.00) |
0.573 (1.00) |
0.588 (1.00) |
0.284 (1.00) |
0.224 (1.00) |
0.24 (1.00) |
0.577 (1.00) |
0.504 (1.00) |
0.00731 (1.00) |
2p loss | 11 (7%) | 154 |
0.756 (1.00) |
0.00649 (1.00) |
0.648 (1.00) |
0.607 (1.00) |
0.491 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.585 (1.00) |
0.343 (1.00) |
0.719 (1.00) |
0.255 (1.00) |
1 (1.00) |
2q loss | 6 (4%) | 159 |
0.335 (1.00) |
0.0267 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.0649 (1.00) |
0.773 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0279 (1.00) |
|
3p loss | 15 (9%) | 150 |
0.00257 (1.00) |
0.673 (1.00) |
0.0444 (1.00) |
0.154 (1.00) |
0.208 (1.00) |
0.0183 (1.00) |
0.0544 (1.00) |
0.0758 (1.00) |
0.0936 (1.00) |
0.0122 (1.00) |
0.0537 (1.00) |
0.115 (1.00) |
3q loss | 10 (6%) | 155 |
0.064 (1.00) |
0.516 (1.00) |
0.0444 (1.00) |
0.391 (1.00) |
0.166 (1.00) |
0.0396 (1.00) |
0.11 (1.00) |
0.00277 (1.00) |
0.0437 (1.00) |
0.0205 (1.00) |
0.0808 (1.00) |
0.118 (1.00) |
4p loss | 59 (36%) | 106 |
0.153 (1.00) |
0.6 (1.00) |
0.621 (1.00) |
0.518 (1.00) |
0.458 (1.00) |
0.942 (1.00) |
0.517 (1.00) |
0.381 (1.00) |
0.0225 (1.00) |
0.402 (1.00) |
0.286 (1.00) |
0.782 (1.00) |
4q loss | 66 (40%) | 99 |
0.0771 (1.00) |
0.918 (1.00) |
0.56 (1.00) |
0.557 (1.00) |
0.736 (1.00) |
0.8 (1.00) |
0.339 (1.00) |
0.253 (1.00) |
0.0382 (1.00) |
0.25 (1.00) |
0.535 (1.00) |
1 (1.00) |
5p loss | 26 (16%) | 139 |
0.212 (1.00) |
0.93 (1.00) |
0.71 (1.00) |
0.846 (1.00) |
0.472 (1.00) |
0.948 (1.00) |
0.0916 (1.00) |
0.696 (1.00) |
0.24 (1.00) |
1 (1.00) |
0.241 (1.00) |
1 (1.00) |
5q loss | 40 (24%) | 125 |
0.947 (1.00) |
0.145 (1.00) |
0.781 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.64 (1.00) |
0.589 (1.00) |
0.189 (1.00) |
0.0311 (1.00) |
0.571 (1.00) |
0.729 (1.00) |
0.703 (1.00) |
6p loss | 13 (8%) | 152 |
0.0989 (1.00) |
0.732 (1.00) |
0.137 (1.00) |
0.421 (1.00) |
0.0323 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.0613 (1.00) |
0.394 (1.00) |
0.465 (1.00) |
0.236 (1.00) |
0.0834 (1.00) |
6q loss | 22 (13%) | 143 |
0.553 (1.00) |
0.838 (1.00) |
0.0346 (1.00) |
0.428 (1.00) |
0.0808 (1.00) |
0.94 (1.00) |
0.173 (1.00) |
0.0127 (1.00) |
0.582 (1.00) |
0.756 (1.00) |
0.803 (1.00) |
0.131 (1.00) |
7q loss | 3 (2%) | 162 |
0.227 (1.00) |
0.96 (1.00) |
0.683 (1.00) |
0.429 (1.00) |
1 (1.00) |
0.595 (1.00) |
0.227 (1.00) |
1 (1.00) |
1 (1.00) |
0.125 (1.00) |
||
8p loss | 73 (44%) | 92 |
0.0381 (1.00) |
0.0897 (1.00) |
0.906 (1.00) |
0.578 (1.00) |
0.277 (1.00) |
0.604 (1.00) |
0.435 (1.00) |
0.776 (1.00) |
0.407 (1.00) |
0.956 (1.00) |
0.0718 (1.00) |
0.634 (1.00) |
8q loss | 11 (7%) | 154 |
0.758 (1.00) |
0.468 (1.00) |
0.943 (1.00) |
0.373 (1.00) |
0.594 (1.00) |
0.767 (1.00) |
0.0117 (1.00) |
0.602 (1.00) |
1 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.288 (1.00) |
9p loss | 23 (14%) | 142 |
0.196 (1.00) |
0.643 (1.00) |
0.188 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.0548 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
0.0059 (1.00) |
0.505 (1.00) |
0.619 (1.00) |
9q loss | 23 (14%) | 142 |
0.143 (1.00) |
0.6 (1.00) |
0.643 (1.00) |
0.0535 (1.00) |
0.695 (1.00) |
0.135 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
0.00873 (1.00) |
0.821 (1.00) |
0.623 (1.00) |
10p loss | 33 (20%) | 132 |
0.0645 (1.00) |
0.0017 (1.00) |
0.47 (1.00) |
0.689 (1.00) |
0.872 (1.00) |
0.276 (1.00) |
0.699 (1.00) |
0.0252 (1.00) |
0.0951 (1.00) |
0.199 (1.00) |
0.354 (1.00) |
0.729 (1.00) |
10q loss | 38 (23%) | 127 |
0.199 (1.00) |
0.0428 (1.00) |
0.411 (1.00) |
0.801 (1.00) |
0.969 (1.00) |
0.272 (1.00) |
0.458 (1.00) |
0.0786 (1.00) |
0.136 (1.00) |
0.16 (1.00) |
0.646 (1.00) |
0.741 (1.00) |
11p loss | 23 (14%) | 142 |
0.471 (1.00) |
0.865 (1.00) |
0.106 (1.00) |
0.447 (1.00) |
0.283 (1.00) |
0.231 (1.00) |
1 (1.00) |
0.0728 (1.00) |
1 (1.00) |
0.399 (1.00) |
0.0426 (1.00) |
0.164 (1.00) |
11q loss | 30 (18%) | 135 |
0.57 (1.00) |
0.746 (1.00) |
0.723 (1.00) |
0.528 (1.00) |
0.963 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.0404 (1.00) |
0.0742 (1.00) |
0.315 (1.00) |
0.713 (1.00) |
0.166 (1.00) |
12p loss | 22 (13%) | 143 |
0.291 (1.00) |
0.555 (1.00) |
0.744 (1.00) |
0.652 (1.00) |
0.463 (1.00) |
0.729 (1.00) |
0.492 (1.00) |
0.219 (1.00) |
0.582 (1.00) |
1 (1.00) |
0.41 (1.00) |
1 (1.00) |
12q loss | 19 (12%) | 146 |
0.287 (1.00) |
0.195 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.553 (1.00) |
0.541 (1.00) |
0.809 (1.00) |
0.365 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.394 (1.00) |
0.649 (1.00) |
13q loss | 8 (5%) | 157 |
0.976 (1.00) |
0.805 (1.00) |
0.327 (1.00) |
0.602 (1.00) |
0.441 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.626 (1.00) |
0.605 (1.00) |
|
14q loss | 67 (41%) | 98 |
1 (1.00) |
0.858 (1.00) |
0.329 (1.00) |
0.551 (1.00) |
0.241 (1.00) |
0.857 (1.00) |
0.427 (1.00) |
0.0155 (1.00) |
0.688 (1.00) |
0.212 (1.00) |
0.76 (1.00) |
0.393 (1.00) |
15q loss | 73 (44%) | 92 |
0.449 (1.00) |
0.91 (1.00) |
0.315 (1.00) |
0.319 (1.00) |
0.442 (1.00) |
0.815 (1.00) |
0.16 (1.00) |
1 (1.00) |
0.0886 (1.00) |
0.883 (1.00) |
0.0879 (1.00) |
1 (1.00) |
16p loss | 9 (5%) | 156 |
0.573 (1.00) |
0.373 (1.00) |
0.0907 (1.00) |
0.847 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.503 (1.00) |
1 (1.00) |
1 (1.00) |
0.784 (1.00) |
1 (1.00) |
16q loss | 15 (9%) | 150 |
0.613 (1.00) |
0.738 (1.00) |
0.275 (1.00) |
0.813 (1.00) |
0.0132 (1.00) |
0.902 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.441 (1.00) |
0.753 (1.00) |
0.839 (1.00) |
1 (1.00) |
17p loss | 107 (65%) | 58 |
0.746 (1.00) |
0.0761 (1.00) |
0.731 (1.00) |
0.0366 (1.00) |
0.951 (1.00) |
0.268 (1.00) |
0.625 (1.00) |
0.223 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.979 (1.00) |
0.613 (1.00) |
17q loss | 26 (16%) | 139 |
0.244 (1.00) |
0.692 (1.00) |
0.754 (1.00) |
0.485 (1.00) |
0.745 (1.00) |
0.945 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.185 (1.00) |
0.393 (1.00) |
0.219 (1.00) |
18p loss | 128 (78%) | 37 |
0.441 (1.00) |
0.413 (1.00) |
0.426 (1.00) |
0.257 (1.00) |
0.7 (1.00) |
0.287 (1.00) |
1 (1.00) |
0.0294 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.548 (1.00) |
0.122 (1.00) |
18q loss | 138 (84%) | 27 |
0.472 (1.00) |
0.263 (1.00) |
0.25 (1.00) |
0.0494 (1.00) |
0.753 (1.00) |
0.318 (1.00) |
0.674 (1.00) |
0.432 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.646 (1.00) |
0.123 (1.00) |
19p loss | 21 (13%) | 144 |
0.342 (1.00) |
0.769 (1.00) |
0.031 (1.00) |
0.521 (1.00) |
0.284 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.368 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.0916 (1.00) |
1 (1.00) |
19q loss | 20 (12%) | 145 |
0.7 (1.00) |
0.498 (1.00) |
0.0353 (1.00) |
0.255 (1.00) |
0.484 (1.00) |
0.931 (1.00) |
0.475 (1.00) |
0.365 (1.00) |
0.545 (1.00) |
0.614 (1.00) |
0.37 (1.00) |
1 (1.00) |
20p loss | 23 (14%) | 142 |
0.774 (1.00) |
0.361 (1.00) |
0.0896 (1.00) |
0.602 (1.00) |
0.63 (1.00) |
0.942 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.242 (1.00) |
0.522 (1.00) |
0.174 (1.00) |
21q loss | 68 (41%) | 97 |
0.645 (1.00) |
0.491 (1.00) |
0.679 (1.00) |
0.13 (1.00) |
0.276 (1.00) |
0.524 (1.00) |
0.636 (1.00) |
0.242 (1.00) |
0.691 (1.00) |
0.235 (1.00) |
0.186 (1.00) |
1 (1.00) |
22q loss | 58 (35%) | 107 |
0.175 (1.00) |
0.102 (1.00) |
0.457 (1.00) |
0.416 (1.00) |
0.0109 (1.00) |
0.554 (1.00) |
0.871 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.877 (1.00) |
0.125 (1.00) |
1 (1.00) |
xq loss | 25 (15%) | 140 |
0.364 (1.00) |
0.829 (1.00) |
0.438 (1.00) |
0.133 (1.00) |
0.337 (1.00) |
0.618 (1.00) |
0.191 (1.00) |
0.418 (1.00) |
1 (1.00) |
0.541 (1.00) |
0.349 (1.00) |
0.0864 (1.00) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = READ-TP.merged_data.txt
-
Number of patients = 165
-
Number of significantly arm-level cnvs = 78
-
Number of selected clinical features = 12
-
Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.